-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_292212-610096

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for snap_scaffold_19-snap.105-T1
Valid prediction for Augustus_model.g28904.t1
Couldn't classify 294580, 294687
Couldn't classify 298806, 298885
Sorry, prediction pasa_asmbl_21187.p1 fails validation.
(CGT)	 AA	294580-294687	GT	AGG
(GTG)	 AG	295104-295292	GT	ATG
(AGG)	 AG	298264-298326	GT	AGG
(CAT)	 AG	298600-298630	GC	AGG
(CTG)	 AG	298806-298885	GT	ATG
-recovered pasa_asmbl_21187.p1, internal, 295104, 295292
-recovered pasa_asmbl_21187.p1, internal, 298264, 298326
-recovered pasa_asmbl_21187.p1, internal, 298600, 298630
-recovered pasa_asmbl_21187.p1, internal, 298806, 298885
Valid prediction for GlimmerHMM_glimmerT_43496-T1
Valid prediction for snap_scaffold_19-snap.121-T1
Valid prediction for GlimmerHMM_glimmerT_43471-T1
Couldn't classify 302644, 302726
Sorry, prediction pasa_asmbl_21188.p1 fails validation.
(CAC)	 GA	302644-302726	GT	AGG
(CTC)	 AG	302881-302956	GT	ACG
(TAC)	 AG	303444-303603	GT	GGG
(GAA)	 AG	304178-304286	GT	CGG
(AGA)	 AG	306024-306193	GT	AGG
(CTG)	 AG	306742-306833	AG	GAA
-recovered pasa_asmbl_21188.p1, terminal, 306742, 306833
-recovered pasa_asmbl_21188.p1, internal, 302881, 302956
-recovered pasa_asmbl_21188.p1, internal, 303444, 303603
-recovered pasa_asmbl_21188.p1, internal, 304178, 304286
-recovered pasa_asmbl_21188.p1, internal, 306024, 306193
Valid prediction for GlimmerHMM_glimmerT_43469-T1
Valid prediction for snap_scaffold_19-snap.122-T1
Valid prediction for GlimmerHMM_glimmerT_43490-T1
Valid prediction for Augustus_model.g28905.t1
Valid prediction for GlimmerHMM_glimmerT_43499-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.97-T1
Valid prediction for GlimmerHMM_glimmerT_43470-T1
Valid prediction for snap_scaffold_19-snap.90-T1
Valid prediction for snap_scaffold_19-snap.109-T1
Valid prediction for GlimmerHMM_glimmerT_43488-T1
Valid prediction for Augustus_model.g28900.t1
Valid prediction for snap_scaffold_19-snap.104-T1
Valid prediction for GlimmerHMM_glimmerT_43491-T1
Valid prediction for GlimmerHMM_glimmerT_43468-T1
Valid prediction for GlimmerHMM_glimmerT_43504-T1
Valid prediction for GlimmerHMM_glimmerT_43497-T1
Valid prediction for snap_scaffold_19-snap.125-T1
Valid prediction for snap_scaffold_19-snap.84-T1
Valid prediction for snap_scaffold_19-snap.76-T1
Valid prediction for GlimmerHMM_glimmerT_43501-T1
Valid prediction for snap_scaffold_19-snap.118-T1
Valid prediction for HiQ_model.g28898.t1
Valid prediction for snap_scaffold_19-snap.95-T1
Valid prediction for GlimmerHMM_glimmerT_43502-T1
Valid prediction for snap_scaffold_19-snap.72-T1
Valid prediction for snap_scaffold_19-snap.73-T1
Valid prediction for snap_scaffold_19-snap.74-T1
Valid prediction for GlimmerHMM_glimmerT_43472-T1
Valid prediction for Augustus_model.g28903.t1
Valid prediction for snap_scaffold_19-snap.107-T1
Valid prediction for snap_scaffold_19-snap.116-T1
Valid prediction for snap_scaffold_19-snap.87-T1
Valid prediction for Augustus_model.g28897.t1
Valid prediction for snap_scaffold_19-snap.100-T1
Valid prediction for snap_scaffold_19-snap.99-T1
Valid prediction for CodingQuarry_transcript_25570-T1
Valid prediction for snap_scaffold_19-snap.128-T1
Couldn't classify 23957, 24049
Sorry, prediction pasa_asmbl_21185.p1 fails validation.
(ATT)	 GC	23957-24049	GT	TGG
(ACA)	 AG	24347-24442	GT	AGG
(GCA)	 AG	24774-24881	GT	TGG
(GCA)	 AG	24993-25136	GT	AGG
(GAG)	 AG	25436-25609	GT	AGG
(TTT)	 AG	25796-25888	GT	AGG
(AAC)	 AG	25976-26101	GT	AGG
(CCC)	 AG	26803-26886	GT	CAG
(CCT)	 AG	26975-27070	GG	GAG
-recovered pasa_asmbl_21185.p1, terminal, 26975, 27070
-recovered pasa_asmbl_21185.p1, internal, 24347, 24442
-recovered pasa_asmbl_21185.p1, internal, 24774, 24881
-recovered pasa_asmbl_21185.p1, internal, 24993, 25136
-recovered pasa_asmbl_21185.p1, internal, 25436, 25609
-recovered pasa_asmbl_21185.p1, internal, 25796, 25888
-recovered pasa_asmbl_21185.p1, internal, 25976, 26101
-recovered pasa_asmbl_21185.p1, internal, 26803, 26886
Valid prediction for snap_scaffold_19-snap.83-T1
Valid prediction for snap_scaffold_19-snap.92-T1
Valid prediction for snap_scaffold_19-snap.96-T1
Valid prediction for snap_scaffold_19-snap.81-T1
Valid prediction for snap_scaffold_19-snap.101-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for snap_scaffold_19-snap.120-T1
Valid prediction for GlimmerHMM_glimmerT_43503-T1
Valid prediction for snap_scaffold_19-snap.124-T1
Valid prediction for GlimmerHMM_glimmerT_43482-T1
Valid prediction for snap_scaffold_19-snap.88-T1
Valid prediction for GlimmerHMM_glimmerT_43495-T1
Valid prediction for snap_scaffold_19-snap.82-T1
Valid prediction for snap_scaffold_19-snap.91-T1
Valid prediction for snap_scaffold_19-snap.78-T1
Valid prediction for GlimmerHMM_glimmerT_43484-T1
Valid prediction for snap_scaffold_19-snap.123-T1
Valid prediction for snap_scaffold_19-snap.77-T1
Valid prediction for snap_scaffold_19-snap.93-T1
Valid prediction for GlimmerHMM_glimmerT_43483-T1
Valid prediction for snap_scaffold_19-snap.126-T1
Valid prediction for snap_scaffold_19-snap.115-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.103-T1
Valid prediction for GlimmerHMM_glimmerT_43486-T1
Valid prediction for GlimmerHMM_glimmerT_43476-T1
Valid prediction for GlimmerHMM_glimmerT_43481-T1
Valid prediction for snap_scaffold_19-snap.119-T1
Valid prediction for GlimmerHMM_glimmerT_43489-T1
Valid prediction for GlimmerHMM_glimmerT_43477-T1
Valid prediction for snap_scaffold_19-snap.112-T1
Valid prediction for snap_scaffold_19-snap.85-T1
Valid prediction for GlimmerHMM_glimmerT_43474-T1
Valid prediction for snap_scaffold_19-snap.102-T1
Valid prediction for snap_scaffold_19-snap.89-T1
Valid prediction for snap_scaffold_19-snap.71-T1
Valid prediction for snap_scaffold_19-snap.130-T1
Valid prediction for GlimmerHMM_glimmerT_43493-T1
Valid prediction for snap_scaffold_19-snap.113-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g28901.t1
Valid prediction for snap_scaffold_19-snap.94-T1
Valid prediction for snap_scaffold_19-snap.86-T1
Valid prediction for snap_scaffold_19-snap.106-T1
Valid prediction for snap_scaffold_19-snap.117-T1
Valid prediction for snap_scaffold_19-snap.80-T1
Valid prediction for GlimmerHMM_glimmerT_43478-T1
Valid prediction for GlimmerHMM_glimmerT_43485-T1
Valid prediction for Augustus_model.g28902.t1
Valid prediction for snap_scaffold_19-snap.108-T1
Valid prediction for snap_scaffold_19-snap.114-T1
Valid prediction for GlimmerHMM_glimmerT_43492-T1
Valid prediction for Augustus_model.g28899.t1
Valid prediction for snap_scaffold_19-snap.75-T1
Valid prediction for GlimmerHMM_glimmerT_43487-T1
Valid prediction for GlimmerHMM_glimmerT_43480-T1
Valid prediction for GlimmerHMM_glimmerT_43475-T1
Valid prediction for GlimmerHMM_glimmerT_43479-T1
Valid prediction for GlimmerHMM_glimmerT_43498-T1
Valid prediction for GlimmerHMM_glimmerT_43500-T1
Valid prediction for snap_scaffold_19-snap.111-T1
Valid prediction for GlimmerHMM_glimmerT_43494-T1
Valid prediction for GlimmerHMM_glimmerT_43473-T1
Valid prediction for snap_scaffold_19-snap.127-T1
Valid prediction for snap_scaffold_19-snap.98-T1
Valid prediction for snap_scaffold_19-snap.79-T1
Valid prediction for snap_scaffold_19-snap.129-T1
Valid prediction for snap_scaffold_19-snap.110-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27551, rend_intergenic: 22777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29373, rend_intergenic: 28970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45084, rend_intergenic: 29972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84981, rend_intergenic: 68433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91063, rend_intergenic: 88262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98337, rend_intergenic: 93734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100465, rend_intergenic: 99450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101558, rend_intergenic: 100732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120050, rend_intergenic: 102192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128499, rend_intergenic: 120110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163538, rend_intergenic: 140151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169788, rend_intergenic: 166298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184726, rend_intergenic: 170492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186628, rend_intergenic: 185324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192237, rend_intergenic: 187350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203073, rend_intergenic: 194248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227466, rend_intergenic: 203245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241912, rend_intergenic: 227466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258786, rend_intergenic: 247549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 287510, rend_intergenic: 286706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 306833, rend_intergenic: 295571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 315922, rend_intergenic: 308103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 317885
-exon list size: 459


building trellis

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-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 27551, rend_intergenic: 22777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29373, rend_intergenic: 28970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45084, rend_intergenic: 29972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84981, rend_intergenic: 68433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91063, rend_intergenic: 88262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98337, rend_intergenic: 93734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100465, rend_intergenic: 99450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101558, rend_intergenic: 100732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120050, rend_intergenic: 102192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128499, rend_intergenic: 120110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163538, rend_intergenic: 140151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169788, rend_intergenic: 166298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184726, rend_intergenic: 170492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186628, rend_intergenic: 185324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192237, rend_intergenic: 187350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203073, rend_intergenic: 194248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227466, rend_intergenic: 203245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241912, rend_intergenic: 227466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258786, rend_intergenic: 247549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 287510, rend_intergenic: 286706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 306833, rend_intergenic: 295571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 315922, rend_intergenic: 308103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support